3-88139639-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001350134.2(ZNF654):āc.1970A>Gā(p.His657Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001350134.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF654 | NM_001350134.2 | c.1970A>G | p.His657Arg | missense_variant | 8/9 | ENST00000636215.2 | NP_001337063.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF654 | ENST00000636215.2 | c.1970A>G | p.His657Arg | missense_variant | 8/9 | 5 | NM_001350134.2 | ENSP00000490842.1 | ||
CGGBP1 | ENST00000462901.5 | c.-229+1331T>C | intron_variant | 1 | ENSP00000418769.1 | |||||
CGGBP1 | ENST00000467332.1 | c.-24+1331T>C | intron_variant | 4 | ENSP00000419459.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 245214Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133182
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460696Hom.: 0 Cov.: 49 AF XY: 0.0000110 AC XY: 8AN XY: 726562
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 17, 2024 | The c.329A>G (p.H110R) alteration is located in exon 1 (coding exon 1) of the ZNF654 gene. This alteration results from a A to G substitution at nucleotide position 329, causing the histidine (H) at amino acid position 110 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at